Ideally each group should be giving you the following group and temporary buffs, though this being LDL I suspect not everyone in your raid force is sitting at 100 AA

:
Group 1
INT Buff (Fury)
Vim (Fury)
INT Buff (Wiz/Illus)
Aria of Acclimation (Troub)
Precision of the Maestro (Troub)
Synergism (Illus)
Frigid Gift (Wiz)
Propagation (Warlock - Proc increase)
Group 2
INT Buff (Illus)
Synergism (Illus)
Time Compression (Illus)
Luck of the Dirge (Dirge - Proc increase)
Should obviously be parsing higher in group 1, but not by 500-600. From what you are saying about parsing really low on some fights, you were probably just unlucky and getting bit by the pet LOS bug quite frequently that trip without noticing. Used to get that myself a lot in FTH before I figured out what the problem was.
Basically, if the line of sight between your pet and the mob is blocked when you tell it to attack, it will go into its attack stance but not cast anything. This can sometimes be a big problem in FTH with all the pillars and doorways if you send your pet in too early. If this happens, telling your pet to attack again won't fix it. Casting Call Servant seems to be the only way to break the bug. Check the parse breakdown of the fights where you parsed abnormally low - I bet your pet's spells and procs are either very low or not showing up at all. Using Call Servant while positioning yourself for the pull, and waiting until you have a good line of sight on the mob to send you pet in will pretty much eliminate this problem.